Background Observational studies in South Asian populations have suggested an association between vitamin B 12 status and metabolic traits; however, the findings have been inconclusive. Hence, the aim of the present study was to use a genetic approach to explore the relationship between metabolic traits and vitamin B 12 status in a Sri Lankan population and to investigate whether these relationships were modified by dietary intake. Methods A total of 109 Sinhalese adults (61 men and 48 women aged 25-50 years) from Colombo City underwent anthropometric and biochemical measurements, dietary intake analysis, and genetic tests. Genetic risk scores (GRS) based on 10 metabolic single nucleotide polymorphisms (SNPs) (metabolic-GRS) and 10 vitamin B 12 SNPs (B12-GRS) were constructed. Results The B12-GRS was significantly associated with serum vitamin B 12 (p = 0.008) but not with metabolic traits (p > 0.05), whereas the metabolic-GRS had no effect on metabolic traits (p > 0.05) and vitamin B 12 concentrations (p > 0.05). An interaction was observed between B12-GRS and protein energy intake (%) on waist circumference (p = 0.002). Interactions were also seen between the metabolic-GRS and carbohydrate energy intake (%) on waist-to-hip ratio (p = 0.015). Conclusion Our findings suggest that a genetically lowered vitamin B 12 concentration may have an impact on central obesity in the presence of a dietary influence; however, our study failed to provide evidence for an impact of metabolic-GRS on lowering B 12 concentrations. Given that our study has a small sample size, further large studies are required to confirm our findings. Keywords SNP. Body mass index. Obesity. Metabolic traits. Vitamin B 12 pathway. Sinhalese. Sri Lanka. Nutrigenetics Abbreviations SNPs Single nucleotide polymorphisms MTHFR Methylenetetrahydrofolate reductase CPS1 Carbamoyl-phosphate synthase 1 CUBN Cubulin CD320 CD320 molecule Electronic supplementary material The online version of this article (